76
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Calabrò RS, Müller-Eising C, Diliberti ML, Manuli A, Parrinello F, Rao G, Barone V, Civello T. Who Will Pay for Robotic Rehabilitation? The Growing Need for a Cost-effectiveness Analysis. INNOVATIONS IN CLINICAL NEUROSCIENCE 2020; 17:14-16. [PMID: 33898096 PMCID: PMC7819581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The robot-assisted rehabilitation is a type of technology that has shown great advances in recent years, demonstrating its effectiveness in different neurological disorders; however, the main argument against the introduction of robot technology in rehabilitation is economic considerations. Herein, we discussed the main concerns related to the widespread use of innovation technology and the need for a cost-effectiveness analysis to enter robotics into the framework of the healthcare systems involved in neurorehabilitation.
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77
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Mancini G, Fusè M, Lazzari F, Chandramouli B, Barone V. Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm. J Chem Phys 2020; 153:124110. [DOI: 10.1063/5.0018314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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78
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Paoloni L, Fusè M, Baiardi A, Barone V. Interplay of Stereoelectronic and Vibrational Modulation Effects in Tuning the UPS Spectra of Unsaturated Hydrocarbon Cage Compounds. J Chem Theory Comput 2020; 16:5218-5226. [PMID: 32667793 PMCID: PMC8009518 DOI: 10.1021/acs.jctc.0c00645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 11/28/2022]
Abstract
The UPS spectra of six hydrocarbon cage compounds have been investigated by a Green-function approach in conjunction with a full harmonic treatment of vibrational modulation effects. The remarkable agreement with experimental results points out the reliability of the proposed computational approach and the strong interplay of stereoelectronic and vibrational effects in tuning the overall spectra.
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79
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Mancini G, Del Galdo S, Chandramouli B, Pagliai M, Barone V. Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics. J Chem Theory Comput 2020; 16:5747-5761. [PMID: 32697580 PMCID: PMC8009517 DOI: 10.1021/acs.jctc.0c00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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Multiscale QM/MM approaches have
become the most suitable and effective
methods for the investigation of spectroscopic properties of medium-
or large-size chromophores in condensed phases. On these grounds,
we are developing a novel workflow aimed at improving the generality,
reliability, and ease of use of the available tools. In the present
paper, we report the latest developments of such an approach with
specific reference to a general workplan starting with the addition
of acetonitrile to the panel of solvents already available in the
General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic
boundary conditions (NPBC). Next, the solvatochromic shifts induced
by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine)
chromophores have been studied introducing in our software a number
of new features ranging from rigid-geometry NPBC molecular dynamics
based on the quaternion formalism to a full integration of variational
(ONIOM) and perturbative (perturbed matrix method (PMM)) approaches
for describing different solute–solvent topologies and local
fluctuations, respectively. Finally, thymine and uracil have been
studied also in methanol to point out the generality of the computational
strategy. While further developments are surely needed, the strengths
of our integrated approach even in its present version are demonstrated
by the accuracy of the results obtained by an unsupervised approach
and coupled to a computational cost strongly reduced with respect
to that of conventional QM/MM models without any appreciable accuracy
deterioration.
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80
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Salta Z, Kosmas AM, Segovia ME, Kieninger M, Tasinato N, Barone V, Ventura ON. Reinvestigation of the Deceptively Simple Reaction of Toluene with OH and the Fate of the Benzyl Radical: The "Hidden" Routes to Cresols and Benzaldehyde. J Phys Chem A 2020; 124:5917-5930. [PMID: 32543200 PMCID: PMC8008427 DOI: 10.1021/acs.jpca.0c03727] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In a previous work, we have investigated the initial steps of the reaction of toluene with the hydroxyl radical using several quantum chemical approaches including density functional and composite post-Hartree-Fock models. Comparison of H-abstraction from the methyl group and additions at different positions of the phenyl ring showed that the former reaction channel is favored at room temperature. This conclusion appears at first sight incompatible with the experimental observation of a lower abundance of the product obtained from abstraction (benzaldehyde) with respect to those originating from addition (cresols). Further reactions of the intermediate radicals with oxygen, water, and additional OH radicals are explored in this paper through theoretical calculations on more than 120 species on the corresponding potential energy surface. The study of the addition reactions, to obtain the cresols through hydroxy methylcyclodienyl intermediate radicals, showed that only in the case of o-cresol the reaction proceeds by addition of O2 to the ring, internal H-transfer, and hydroperoxyl abstraction and not through direct H-abstraction. For both p- and m-cresol, instead, the reaction occurs through a higher-energy direct H-abstraction, thus explaining in part the observed larger concentration of the ortho isomer in the final products. It was also found that the benzyl radical, formed by H-abstraction from the methyl group, is able to react further if additional OH is present. Two reaction paths leading to o-cresol, two leading to p-cresol, and one leading to m-cresol were determined. Moreover, in this situation, the benzyl radical is predicted to produce benzyl alcohol, as was found in some experiments. The commonly accepted route to benzaldehyde was found to be not the energetically favored one. Instead, a route leading to the benzoyl radical (and ultimately to benzoic acid) with the participation of one water molecule was clearly more favorable, both thermodynamically and kinetically.
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81
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Lupi J, Puzzarini C, Cavallotti C, Barone V. State-of-the-Art Quantum Chemistry Meets Variable Reaction Coordinate Transition State Theory to Solve the Puzzling Case of the H 2S + Cl System. J Chem Theory Comput 2020; 16:5090-5104. [PMID: 32603107 PMCID: PMC8009477 DOI: 10.1021/acs.jctc.0c00354] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The atmospheric reaction of H2S with Cl has been reinvestigated to check if, as previously suggested, only explicit dynamical computations can lead to an accurate evaluation of the reaction rate because of strong recrossing effects and the breakdown of the variational extension of transition state theory. For this reason, the corresponding potential energy surface has been thoroughly investigated, thus leading to an accurate characterization of all stationary points, whose energetics has been computed at the state of the art. To this end, coupled-cluster theory including up to quadruple excitations has been employed, together with the extrapolation to the complete basis set limit and also incorporating core-valence correlation, spin-orbit, and scalar relativistic effects as well as diagonal Born-Oppenheimer corrections. This highly accurate composite scheme has also been paralleled by less expensive yet promising computational approaches. Moving to kinetics, variational transition state theory and its variable reaction coordinate extension for barrierless steps have been exploited, thus obtaining a reaction rate constant (8.16 × 10-11 cm3 molecule-1 s-1 at 300 K and 1 atm) in remarkable agreement with the experimental counterpart. Therefore, contrary to previous claims, there is no need to invoke any failure of the transition state theory, provided that sufficiently accurate quantum-chemical computations are performed. The investigation of the puzzling case of the H2S + Cl system allowed us to present a robust approach for disclosing the thermochemistry and kinetics of reactions of atmospheric and astrophysical interest.
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82
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Del Galdo S, Fusè M, Barone V. CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach. Front Chem 2020; 8:584. [PMID: 32733856 PMCID: PMC7358700 DOI: 10.3389/fchem.2020.00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022] Open
Abstract
We extend a recently proposed computational strategy for the simulation of absorption spectra of semi-rigid molecular systems in condensed phases to the emission spectra of flexible chromophores. As a case study, we have chosen the CPL spectrum of camphor in methanol solution, which shows a well-defined bisignate shape. The first step of our approach is the quantum mechanical computation of reference spectra including vibrational averaging effects and taking bulk solvent effects into account by means of the polarizable continuum model. In the present case, the large amplitude inversion mode is explicitly treated by a numerical approach, whereas the other small-amplitude vibrational modes are taken into account within the harmonic approximation. Next, the snapshots of classical molecular dynamics computations are clusterized and one representative configuration from each cluster is used to compute a reference spectrum. In the present case, different clusters correspond to the two stable conformers of camphor in the S1 excited electronic state and, for each of them, to different numbers of strong solute-solvent hydrogen bonds. Finally, local fluctuation effects within each cluster are taken into account by means of the perturbed matrix model. The overall procedure leads to good agreement with experiment for absorption and emission spectra together with their chiral counterparts, thus allowing to analyze the role of different effects (stereo-electronic, vibrational, environmental) in tuning the overall experimental spectra.
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83
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Ye H, Mendolicchio M, Kruse H, Puzzarini C, Biczysko M, Barone V. The challenging equilibrium structure of HSSH: Another success of the rotational spectroscopy / quantum chemistry synergism. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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84
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Baiano C, Lupi J, Tasinato N, Puzzarini C, Barone V. The Role of State-of-the-Art Quantum-Chemical Calculations in Astrochemistry: Formation Route and Spectroscopy of Ethanimine as a Paradigmatic Case. Molecules 2020; 25:E2873. [PMID: 32580443 PMCID: PMC7357107 DOI: 10.3390/molecules25122873] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022] Open
Abstract
The gas-phase formation and spectroscopic characteristics of ethanimine have been re-investigated as a paradigmatic case illustrating the accuracy of state-of-the-art quantum-chemical (QC) methodologies in the field of astrochemistry. According to our computations, the reaction between the amidogen, NH, and ethyl, C2H5, radicals is very fast, close to the gas-kinetics limit. Although the main reaction channel under conditions typical of the interstellar medium leads to methanimine and the methyl radical, the predicted amount of the two E,Z stereoisomers of ethanimine is around 10%. State-of-the-art QC and kinetic models lead to a [E-CH3CHNH]/[Z-CH3CHNH] ratio of ca. 1.4, slightly higher than the previous computations, but still far from the value determined from astronomical observations (ca. 3). An accurate computational characterization of the molecular structure, energetics, and spectroscopic properties of the E and Z isomers of ethanimine combined with millimeter-wave measurements up to 300 GHz, allows for predicting the rotational spectrum of both isomers up to 500 GHz, thus opening the way toward new astronomical observations.
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85
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Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
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86
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Onofri S, Balucani N, Barone V, Benedetti P, Billi D, Balbi A, Brucato JR, Cobucci-Ponzano B, Costanzo G, Rocca NL, Moracci M, Saladino R, Vladilo G. The Italian National Project of Astrobiology-Life in Space-Origin, Presence, Persistence of Life in Space, from Molecules to Extremophiles. ASTROBIOLOGY 2020; 20:580-582. [PMID: 32364794 PMCID: PMC7232638 DOI: 10.1089/ast.2020.2247] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
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87
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Del Galdo S, Fusè M, Barone V. The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study. J Chem Theory Comput 2020; 16:3294-3306. [PMID: 32250614 PMCID: PMC7222099 DOI: 10.1021/acs.jctc.0c00124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
This paper deals
with the development and first validation of a
composite approach for the simulation of chiroptical spectra in solution
aimed to strongly reduce the number of full QM computations without
any significant accuracy loss. The approach starts from the quantum
mechanical computation of reference spectra including vibrational
averaging effects and taking average solvent effects into account
by means of the polarizable continuum model. Next, the snapshots of
classical molecular dynamics computations are clusterized and one
reference configuration from each cluster is used to compute a reference
spectrum. Local fluctuation effects within each cluster are then taken
into account by means of the perturbed matrix model. The performance
of the proposed approach is tested on the challenging case of the
optical and chiroptical spectra
of camphorquinone in methanol solution. Although further validations
are surely needed, the results of this first study are quite promising
also taking into account that agreement with experimental data is
reached by just a couple of full quantum mechanical geometry optimizations
and frequency computations.
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88
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Lazzari F, Salvadori A, Mancini G, Barone V. Molecular Perception for Visualization and Computation: The Proxima Library. J Chem Inf Model 2020; 60:2668-2672. [PMID: 32271572 PMCID: PMC7997373 DOI: 10.1021/acs.jcim.0c00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https://bitbucket.org/sns-smartlab/proxima/src/master/.
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89
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Biswas AD, Barone V, Amadei A, Daidone I. Length-scale dependence of protein hydration-shell density. Phys Chem Chem Phys 2020; 22:7340-7347. [PMID: 32211621 DOI: 10.1039/c9cp06214a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here we present a computational approach based on molecular dynamics (MD) simulation to study the dependence of the protein hydration-shell density on the size of the protein molecule. The hydration-shell density of eighteen different proteins, differing in size, shape and function (eight of them are antifreeze proteins), is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4-14%) for all studied proteins and that this increment strongly correlates with the protein size. In particular, a decrease in the density increment is observed for decreasing protein size. A simple model is proposed in which the basic idea is to approximate the protein molecule as an effective ellipsoid and to partition the relevant parameters, i.e. the solvent-accessible volume and the corresponding solvent density, into two regions: inside and outside the effective protein ellipsoid. It is found that, within the model developed here, almost all of the hydration-density increase is located inside the protein ellipsoid, basically corresponding to pockets within, or at the surface of the protein molecule. The observed decrease in the density increment is caused by the protein size only and no difference is found between antifreeze and non-antifreeze proteins.
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90
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Boussessi R, Tasinato N, Pietropolli Charmet A, Stoppa P, Barone V. Sextic centrifugal distortion constants: interplay of density functional and basis set for accurate yet feasible computations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1734678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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91
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Martino M, Salvadori A, Lazzari F, Paoloni L, Nandi S, Mancini G, Barone V, Rampino S. Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality. J Comput Chem 2020; 41:1310-1323. [PMID: 32058615 DOI: 10.1002/jcc.26172] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 01/28/2023]
Abstract
The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.
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92
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Melosso M, Melli A, Spada L, Zheng Y, Chen J, Li M, Lu T, Feng G, Gou Q, Dore L, Barone V, Puzzarini C. Rich Collection of n-Propylamine and Isopropylamine Conformers: Rotational Fingerprints and State-of-the-Art Quantum Chemical Investigation. J Phys Chem A 2020; 124:1372-1381. [PMID: 31985228 PMCID: PMC7997563 DOI: 10.1021/acs.jpca.9b11767] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
The
conformational isomerism of isopropylamine and n-propylamine
has been investigated by means of an integrated strategy combining
high-level quantum-chemical calculations and high-resolution rotational
spectroscopy. The equilibrium structures (and thus equilibrium rotational
constants) as well as relative energies of all conformers have been
computed using the so-called “cheap” composite scheme,
which combines the coupled-cluster methodology with second-order Møller–Plesset
perturbation theory for extrapolation to the complete basis set. Methods
rooted in the density functional theory have been instead employed
for computing spectroscopic parameters and for accounting for vibrational
effects. Guided by quantum-chemical predictions, the rotational spectra
of isopropylamine and n-propylamine have been investigated between
2 and 400 GHz with Fourier transform microwave and frequency-modulation
millimeter/submillimeter spectrometers. Spectral assignments confirmed
the presence of several conformers with comparable stability and pointed
out possible Coriolis resonance effects between some of them.
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93
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Paoloni L, Mazzeo G, Longhi G, Abbate S, Fusè M, Bloino J, Barone V. Toward Fully Unsupervised Anharmonic Computations Complementing Experiment for Robust and Reliable Assignment and Interpretation of IR and VCD Spectra from Mid-IR to NIR: The Case of 2,3-Butanediol and trans-1,2-Cyclohexanediol. J Phys Chem A 2020; 124:1011-1024. [PMID: 31922423 PMCID: PMC7993639 DOI: 10.1021/acs.jpca.9b11025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
The infrared (IR)
and vibrational circular dichroism (VCD) spectra
of 2,3-butanediol and trans-1,2-cyclohexanediol from
900 to 7500 cm–1 (including mid-IR, fundamental
CH and OH stretchings, and near-infrared regions) have been investigated
by a combined experimental and computational strategy. The computational
approach is rooted in density functional theory (DFT) computations
of harmonic and leading anharmonic mechanical, electrical, and magnetic
contributions, followed by a generalized second-order perturbative
(GVPT2) evaluation of frequencies and intensities for all the above
regions without introducing any ad hoc scaling factor. After proper
characterization of large-amplitude motions, all resonances plaguing
frequencies and intensities are taken into proper account. Comparison
of experimental and simulated spectra allows unbiased assignment and
interpretation of the most interesting features. The reliability of
the GVPT2 approach for OH stretching fundamentals and overtones is
confirmed by the remarkable agreement with a local mode model purposely
tailored for the latter two regions. Together with the specific interest
of the studied molecules, our results confirm that an unbiased assignment
and interpretation of vibrational spectra for flexible medium-size
molecules can be achieved by means of a nearly unsupervised reliable,
robust, and user-friendly DFT/GVPT2 model.
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94
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Vieira Pinto SM, Tasinato N, Barone V, Amadei A, Zanetti-Polzi L, Daidone I. Modeling amino-acid side chain infrared spectra: the case of carboxylic residues. Phys Chem Chem Phys 2020; 22:3008-3016. [DOI: 10.1039/c9cp04774c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.
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95
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Potenti S, Paoloni L, Nandi S, Fusè M, Barone V, Rampino S. Chemical bonding in cuprous complexes with simple nitriles: octet rule and resonance concepts versus quantitative charge-redistribution analysis. Phys Chem Chem Phys 2020; 22:20238-20247. [DOI: 10.1039/d0cp01536a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Resonance structures for six cuprous complexes with simple nitriles are interpreted by means of a quantitative analysis of charge redistribution upon copper-nitrile bonding.
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96
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Chen J, Zheng Y, Melli A, Spada L, Lu T, Feng G, Gou Q, Barone V, Puzzarini C. Theory meets experiment for elucidating the structure and stability of non-covalent complexes: water–amine interaction as a proof of concept. Phys Chem Chem Phys 2020; 22:5024-5032. [DOI: 10.1039/c9cp06768j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A joint experimental-theoretical spectroscopic investigation has focused on a better understanding of the nature of weak, non-covalent interactions in amine-water model systems.
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97
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Puzzarini C, Barone V. The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy. Phys Chem Chem Phys 2020; 22:6507-6523. [PMID: 32163090 DOI: 10.1039/d0cp00561d] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.
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98
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Alessandrini S, Barone V, Puzzarini C. Extension of the “Cheap” Composite Approach to Noncovalent Interactions: The jun-ChS Scheme. J Chem Theory Comput 2019; 16:988-1006. [DOI: 10.1021/acs.jctc.9b01037] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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99
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Puzzarini C, Barone V. Challenges in astrochemistry: The spectroscopic point of view: Comment on "Prebiotic chemistry and origins of life research with atomistic computer simulations" by A. Pérez-Villa, F. Pietrucci, and A.M. Saitta. Phys Life Rev 2019; 34-35:143-146. [PMID: 31761732 DOI: 10.1016/j.plrev.2019.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 11/29/2022]
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100
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Fusè M, Mazzeo G, Longhi G, Abbate S, Masi M, Evidente A, Puzzarini C, Barone V. Unbiased Determination of Absolute Configurations by vis-à-vis Comparison of Experimental and Simulated Spectra: The Challenging Case of Diplopyrone. J Phys Chem B 2019; 123:9230-9237. [PMID: 31580674 DOI: 10.1021/acs.jpcb.9b08375] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new experimental-computational strategy for the determination of the absolute configuration (AC) of complex chiral molecules is proposed by combining diverse experimental spectroscopies with quantum-mechanical simulations well beyond the current computational practice. Key features are the conformer search and relative stability evaluation performed by a new stochastic two-level tool followed by a vis-à-vis comparison of experimental and computed spectra without any ad hoc adjustment. The entire computational procedure is embedded in the user-friendly VMS software, and its reliability is granted by the inclusion of mechanic/electric/magnetic anharmonicity as well as ro-vibrational and vibronic couplings by means of generalized perturbation theory in conjunction with double-hybrid functionals combined with empirical dispersion contributions and suitable basis sets. To test and validate the new approach, the puzzling case of diplopyrone, a fungal phytotoxic metabolite, has been chosen: the close match between new experimental and simulated infrared absorption and vibrational circular dichroism spectra has led to the unbiased evaluation of its AC.
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